[Debian-med-packaging] Bug#815174: staden: Missing links in /usr/bin

[Andreas Tille]

Hi Kerstin,

thanks a lot for this bug report which is really appreciated as well as
the analysis of the error and the hint for a fix.  I've not decided
whether we really should provide eba itself in /usr/bin or whether it
might be better to use wrapper scripts setting the PATH to
/usr/lib/staden/bin.  The question is whether eba is a user oriented
application itself or just an internal helper.

Trusting your insight as a user I wonder what you might think about
the role of eba.

Kind regards

     Andreas.

On Fri, Feb 19, 2016 at 06:48:41PM +0100, Kerstin Hoef-Emden wrote:
> Package: staden
> Version: 2.0.0+b10-1.1
> Severity: grave
> Justification: renders package unusable
> 
> Dear Maintainer,
> 
> I tried to convert *.ab1 files to *.exp files with pregap4, which failed
> with an error message that eba could not be found. I copied an eba from the sourceforge download bay into /usr/bin and retried
> conversion of the ABI chromatograms. The error message concerning eba was
> gone, instead conversion failed because of a missing init_exp command.
> Thereafter I had a closer look into /usr/bin and realized that the staden
> parts were links to /usr/lib/staden/bin, but of the multiple files in
> the sourceforge package, only pregap, gap4, gap5, trev and spin had such a link.
> 
> I thus, created the missing links by hand and conversion worked out. The
> files could be opened and assembled with gap4. Working furtheron with the
> files, however, is still hampered by another problem, which I suspect to be
> of a different kind, thus will be subject to a separate bug report.
> 
> Kerstin
> 
> 
> -- System Information:
> Debian Release: 8.3
>   APT prefers stable-updates
>   APT policy: (500, 'stable-updates'), (500, 'stable')
> Architecture: i386 (i686)
> 
> Kernel: Linux 3.2.0-4-686-pae (SMP w/2 CPU cores)
> Locale: LANG=de_DE.utf8, LC_CTYPE=de_DE.utf8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> Init: systemd (via /run/systemd/system)
> 
> Versions of packages staden depends on:
> ii  libc6                2.19-18+deb8u3
> ii  libcurl3             7.38.0-4+deb8u3
> ii  libfontconfig1       2.11.0-6.3
> ii  libfreetype6         2.5.2-3+deb8u1
> ii  libgcc1              1:4.9.2-10
> ii  liblzma5             5.1.1alpha+20120614-2+b3
> ii  libpng12-0           1.2.50-2+deb8u2
> ii  libstaden-read1      1.13.7-1
> ii  libstdc++6           4.9.2-10
> ii  libtcl8.6            8.6.2+dfsg-2
> ii  libtk8.6             8.6.2-1
> ii  libx11-6             2:1.6.2-3
> ii  libxext6             2:1.3.3-1
> ii  libxft2              2.3.2-1
> ii  libxss1              1:1.2.2-1
> ii  staden-common        2.0.0+b10-1.1
> ii  staden-io-lib-utils  1.13.7-1
> ii  tklib                0.6-1
> ii  zlib1g               1:1.2.8.dfsg-2+b1
> 
> staden recommends no packages.
> 
> Versions of packages staden suggests:
> pn  staden-doc  <none>
> 
> -- no debconf information
> 
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